Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity

Álvarez, Daniel; Sapia, Jennifer L.

doi:10.1016/j.ceb.2023.102205

Cited by 6 publications

(4 citation statements)

References 64 publications

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“…The obtained trajectory is analogous to a movie of the many particles involved as they reorganize in time toward convoluted and sometimes unexpected configurations. Particularly, molecular dynamics has become an essential tool to investigate the molecular properties of membrane trafficking processes …”

Section: Resultsmentioning

confidence: 99%

“…Cristae in mitochondria or trafficking intracellular vesicles are common examples of their variety and functional versatility. Their innate dynamical behavior, due to the fluid nature of lipid assemblies, has historically complicated the study of its mesoscopic morphologies at or near equilibrium. Furthermore, due to space restrictions, confined vesicles may produce a myriad of multivesicular structures difficult to predict in three dimensions.…”

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confidence: 99%

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The Secret Ballet Inside Multivesicular Bodies

Mayorga,

Masone

2024

ACS Nano

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Lipid bilayers possess the capacity for selfassembly due to the amphipathic nature of lipid molecules, which have both hydrophobic and hydrophilic regions. When confined, lipid bilayers exhibit astonishing versatility in their forms, adopting diverse shapes that are challenging to observe through experimental means. Exploiting this adaptability, lipid structures motivate the development of bio-inspired mechanomaterials and integrated nanobio-interfaces that could seamlessly merge with biological entities, ultimately bridging the gap between synthetic and biological systems. In this work, we demonstrate how, in numerical simulations of multivesicular bodies, a fascinating evolution unfolds from an initial semblance of order toward states of higher entropy over time. We observe dynamic rearrangements in confined vesicles that reveal unexpected limit shapes of distinct geometric patterns. We identify five structures as the basic building blocks that systematically repeat under various conditions of size and composition. Moreover, we observe more complex and less frequent shapes that emerge in confined spaces. Our results provide insights into the dynamics of multivesicular systems, offering a richer understanding of how confined lipid bodies spontaneously self-organize.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

The Secret Ballet Inside Multivesicular Bodies

Mayorga,

Masone

2024

ACS Nano

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“…CG molecular dynamics (MD) simulations have become a popular method in studying biological processes with time and length scales beyond the reach of AA-MD simulations, [1][2][3][4][5][6] such as large-scale membrane deformation, organelle biogenesis, and the complete virion or capsid of a virus. [7][8][9][10] In this context, resolution transformation from CG to AA, or backmapping, is necessary to obtain detailed atomistic interactions between molecules, a level of detail not available in CG resolution.…”

Section: Introductionmentioning

confidence: 99%

Backmapping with Mapping and Isomeric Information

Kim

2023

Preprint

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I present a powerful and flexible backmapping tool named Multiscale Simulation Tool (mstool) that converts a coarse-grained (CG) system into all-atom (AA) resolution and only requires AA to CG mapping and isomeric information (cis/trans/chiral). The backmapping procedure includes two simple steps: a) the AA atoms are randomly placed near the corresponding CG beads according to the provided mapping scheme. b) the energy minimization is performed with two modifications in the forcefield. First, the nonbonded interactions are replaced with a cosine function to ensure numerical stability. Second, additional dihedrals are imposed to maintain the molecule's isomeric properties. To test the tool's simplicity and robustness, I have demonstrated a backmapping of the four-bead CG lipid model into the corresponding AA resolution (resolution increased by a factor of 34) without using an intermediate resolution. The tool is freely available at github.com/ksy141/mstool.

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“…CG molecular dynamics (MD) simulations have become a popular method in studying biological processes with time and length scales beyond the reach of AA-MD simulations, − such as large-scale membrane deformation, organelle biogenesis, and the complete virion or capsid of a virus. − In this context, resolution transformation from CG to AA, or backmapping, is necessary to obtain detailed atomistic interactions between molecules, a level of detail not available in CG resolution. Therefore, CG-MD and backmapping can complement each other: one can perform preliminary CG-MD simulations to navigate the systems’ equilibrium distribution, followed by additional AA-MD simulations, using initial structures obtained from backmapping.…”

Section: Introductionmentioning

confidence: 99%

Backmapping with Mapping and Isomeric Information

Kim

2023

J. Phys. Chem. B

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Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity

Cited by 6 publications

References 64 publications

The Secret Ballet Inside Multivesicular Bodies

The Secret Ballet Inside Multivesicular Bodies

Backmapping with Mapping and Isomeric Information

Backmapping with Mapping and Isomeric Information

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